jabref IllegalArgumentException: URI is not absolute

JabRef version

Latest development branch build (please note build date below)

Operating system

GNU / Linux

Details on version and operating system

JabRef 6.0--2024-11-05--4705977 Linux 6.1.0-26-amd64 amd64 Java 21.0.5 JavaFX 23.0.1+4

Checked with the latest development build (copy version output from About dialog)

[x] I made a backup of my libraries before testing the latest development version.
[x] I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

I've just been using global search.

Unfortunately, I can't quite reproduce this issue, although I've had this exception a few times already. It appears to be related to when I use search, the entry list when a group is selected. Also, it seems to happen after JR has been running for a while.

Appendix

...

Log File

java.lang.IllegalArgumentException: URI is not absolute
	at java.base/java.net.URL.of(Unknown Source)
	at java.base/java.net.URI.toURL(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.convert(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at java.base/java.util.Optional.map(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$1.computeValue(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$1.computeValue(Unknown Source)
	at [email protected]/javafx.beans.binding.ObjectBinding.get(Unknown Source)
	at [email protected]/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$3.computeValue(Unknown Source)
	at [email protected]/javafx.beans.binding.ObjectBinding.get(Unknown Source)
	at [email protected]/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
	at [email protected]/javafx.scene.control.TableCell.updateItem(Unknown Source)
	at [email protected]/javafx.scene.control.TableCell.indexChanged(Unknown Source)
	at [email protected]/javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
	at [email protected]/javafx.scene.control.skin.TableRowSkinBase.updateCells(Unknown Source)
	at [email protected]/javafx.scene.control.skin.TableRowSkinBase.checkState(Unknown Source)
	at [email protected]/javafx.scene.control.skin.TableRowSkinBase.computePrefHeight(Unknown Source)
	at [email protected]/javafx.scene.control.Control.computePrefHeight(Unknown Source)
	at [email protected]/javafx.scene.Parent.prefHeight(Unknown Source)
	at [email protected]/javafx.scene.layout.Region.prefHeight(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.resizeCell(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.getCell(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.getOrCreateCellSize(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.getOrCreateCellSize(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.recalculateAndImproveEstimatedSize(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.recalculateAndImproveEstimatedSize(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.recalculateEstimatedSize(Unknown Source)
	at [email protected]/javafx.scene.control.skin.VirtualFlow.layoutChildren(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Parent.layout(Unknown Source)
	at [email protected]/javafx.scene.Scene.doLayoutPass(Unknown Source)
	at [email protected]/javafx.scene.Scene$ScenePulseListener.pulse(Unknown Source)
	at [email protected]/com.sun.javafx.tk.Toolkit.lambda$runPulse$2(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at [email protected]/com.sun.javafx.tk.Toolkit.runPulse(Unknown Source)
	at [email protected]/com.sun.javafx.tk.Toolkit.firePulse(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.pulseFromQueue(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$11(Unknown Source)
	at [email protected]/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at [email protected]/com.sun.glass.ui.gtk.GtkApplication.enterNestedEventLoopImpl(Native Method)
	at [email protected]/com.sun.glass.ui.gtk.GtkApplication._enterNestedEventLoop(Unknown Source)
	at [email protected]/com.sun.glass.ui.Application.enterNestedEventLoop(Unknown Source)
	at [email protected]/com.sun.glass.ui.EventLoop.enter(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(Unknown Source)
	at [email protected]/javafx.stage.Stage.showAndWait(Unknown Source)
	at [email protected]/javafx.scene.control.HeavyweightDialog.showAndWait(Unknown Source)
	at [email protected]/javafx.scene.control.Dialog.showAndWait(Unknown Source)
	at [email protected]/org.jabref.gui.JabRefDialogService.showConfirmationDialogAndWait(Unknown Source)
	at [email protected]/org.jabref.gui.search.GlobalSearchBar.lambda$initSearchModifierButtons$8(Unknown Source)
	at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(Unknown Source)
	at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
	at [email protected]/javafx.beans.property.BooleanPropertyBase.fireValueChangedEvent(Unknown Source)
	at [email protected]/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
	at [email protected]/javafx.beans.property.BooleanPropertyBase.set(Unknown Source)
	at [email protected]/javafx.scene.control.ToggleButton.setSelected(Unknown Source)
	at [email protected]/org.jabref.gui.search.GlobalSearchBar.lambda$initSearchModifierButtons$14(Unknown Source)
	at [email protected]/com.sun.javafx.collections.SetListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
	at [email protected]/com.sun.javafx.collections.SetListenerHelper.fireValueChangedEvent(Unknown Source)
	at [email protected]/com.sun.javafx.collections.ObservableSetWrapper.callObservers(Unknown Source)
	at [email protected]/com.sun.javafx.collections.ObservableSetWrapper.remove(Unknown Source)
	at [email protected]/org.jabref.logic.search.SearchPreferences.setSearchFlag(Unknown Source)
	at [email protected]/org.jabref.gui.search.GlobalSearchBar.lambda$initSearchModifierButtons$9(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
	at [email protected]/javafx.scene.Node.fireEvent(Unknown Source)
	at [email protected]/javafx.scene.control.ToggleButton.fire(Unknown Source)
	at [email protected]/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
	at [email protected]/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
	at [email protected]/javafx.scene.Scene$MouseHandler.process(Unknown Source)
	at [email protected]/javafx.scene.Scene.processMouseEvent(Unknown Source)
	at [email protected]/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
	at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
	at [email protected]/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
	at [email protected]/com.sun.glass.ui.View.notifyMouse(Unknown Source)
	at [email protected]/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at [email protected]/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$10(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

Nov 12 '24 07:11 ytzemih

It seems to be related to a value in the file field somewhere that cannot be parsed to an URL

Nov 12 '24 10:11 Siedlerchr

That makes sense, though, I haven't seen these exceptions before. Perhaps, the URI parser is now less relaxed? Ok, I'll try to check the file fields and see whether I can find something odd.

Nov 12 '24 13:11 ytzemih

Alright, I can replicate this exception with the following MWE:

@InProceedings{Test,
  author       = {Test},
  title        = {Test},
  file         = {A test:www.yahoo.com/abc/cde.htm:URL},
}

It is derived from an entry existing in my DB, so not constructed. The repair amounts to adding a http://.

Alternatively, you can stimulate this exception with:

Edit the file field of an entry
Add file link
Copy the URL from the snippet into the "Link" field
Choose filetype URL
Press "add"

I suppose that the exception will pop up wherever the URL parser is used. I've had some incomplete URLs in my DB files, but JR 6 now complains.

Nov 13 '24 07:11 ytzemih

After https://github.com/JabRef/jabref/pull/12156/ is merged, we can work on this.

Nov 16 '24 23:11 koppor

/assign-me

Nov 23 '24 19:11 yash-agrawal03

👋 Hey @yash-agrawal03, thank you for your interest in this issue! 🎉

We're excited to have you on board. Start by exploring our Contributing guidelines, and don't forget to check out our workspace setup guidelines to get started smoothly.

In case you encounter failing tests during development, please check our developer FAQs!

Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on JabRef's Gitter chat. And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.

Happy coding! 🚀

⏳ Please note, you will be automatically unassigned if the issue isn't closed within 90 days (by 21 February 2025). A maintainer can also add the "📌 Pinned"" label to prevent automatic unassignment.

Nov 23 '24 19:11 github-actions[bot]

@koppor by when is the pr #12156 expected to close? I have to wait for that PR to get closed right?

Nov 25 '24 17:11 yash-agrawal03

@yash-agrawal03 I worked on it, it is merged now.

Nov 25 '24 21:11 koppor

Thank-You koppor, I will start working on this issue.

Nov 26 '24 17:11 yash-agrawal03

/unassign @yash-agrawal03

Dec 10 '24 13:12 koppor

👋 Hey @yash-agrawal03, you've been automatically unassigned from this issue due to inactivity.

[!NOTE] If you'd like to be re-assigned, just leave another comment or ask a maintainer to assign you again. If you're still actively working on the issue, let us know by commenting, and we can pin it to prevent automatic unassignment.

Dec 10 '24 13:12 github-actions[bot]

/assign-me

Please give me another chance to complete this request

Jan 01 '25 13:01 yash-agrawal03

Hi, I am Yash , a student at King's College London working with @LinusDietz. Could I work on this task?

Feb 06 '25 17:02 yshukla01

/assign @yshukla01

Feb 06 '25 18:02 Siedlerchr

👋 Hey @yshukla01, thank you for your interest in this issue! 🎉

We're excited to have you on board. Start by exploring our Contributing guidelines, and don't forget to check out our workspace setup guidelines to get started smoothly.

In case you encounter failing tests during development, please check our developer FAQs!

Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on JabRef's Gitter chat. And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.

Happy coding! 🚀

⏳ Please note, you will be automatically unassigned if the issue isn't closed within 90 days (by 07 May 2025). A maintainer can also add the "📌 Pinned"" label to prevent automatic unassignment.

Feb 06 '25 18:02 github-actions[bot]

📋 Assignment Update

Hi @yshukla01, you are no longer assigned to this issue.

Next steps

If you still want to work on this:

Comment with /assign-me to request reassignment
Ask a maintainer to assign you again
If you're making progress, a maintainer can add the pin label to prevent future automatic unassignment

Mar 17 '25 12:03 github-actions[bot]

Hello, @koppor I am Fahad can you assign me this task, please?

Mar 21 '25 21:03 sfahaddev

👋 Hey @sfahaddev, looks like you’re eager to work on this issue—great! 🎉 It also looks like you skipped reading our CONTRIBUTING.md, which explains exactly how to participate. No worries, it happens to the best of us. Give it a read, and you’ll discover the ancient wisdom of assigning issues to yourself. Trust me, it’s worth it. 🚀

Mar 21 '25 21:03 github-actions[bot]

/assign-me

Mar 21 '25 21:03 sfahaddev

👋 Hey @sfahaddev, thank you for your interest in this issue! 🎉

We're excited to have you on board. Start by exploring our Contributing guidelines, and don't forget to check out our workspace setup guidelines to get started smoothly.

In case you encounter failing tests during development, please check our developer FAQs!

Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on JabRef's Gitter chat. And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.

Happy coding! 🚀

⏳ Please note, you will be automatically unassigned if there is not a (draft) pull request within 14 days (by 04 April 2025).

Mar 21 '25 21:03 github-actions[bot]

/assign me

May 01 '25 01:05 pranav0510s

⚠️ Issue Already Assigned

Hi @pranav0510s, this issue is currently assigned to @sfahaddev.

[!NOTE] If no progress is made within 14 days, the issue will be automatically unassigned.

Options for contributors

Wait for availability: The issue may become available if auto-unassigned
Collaborate: You can ask the assignee if they want help
Maintainer assistance: A maintainer can add you as co-assignee if appropriate

May 01 '25 01:05 github-actions[bot]

/assign-me

Jun 04 '25 10:06 jenilpatel264

⚠️ Assignment Limit Reached

Hi @jenilpatel264, you've reached the maximum number of 3 concurrent assignments.

[!NOTE] Please complete or unassign from your current issues before taking on new ones.

Current options

Complete one of your assigned issues and close it
Use /unassign-me on an issue you're no longer working on
Ask a maintainer for an exception if this is a special case

Jun 04 '25 10:06 github-actions[bot]

/assign-me

Jun 04 '25 10:06 jenilpatel264

👋 Hey @jenilpatel264, thank you for your interest in this issue! 🎉

We're excited to have you on board. Start by exploring our Contributing guidelines, and don't forget to check out our workspace setup guidelines to get started smoothly.

For questions on JabRef functionality and the code base, you can consult the JabRef Guru or ask on our Gitter chat.

In case you encounter failing tests during development, please check our developer FAQs!

Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on JabRef's Gitter chat. And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.

Happy coding! 🚀

Jun 04 '25 10:06 github-actions[bot]

⏰ Assignment Reminder

Hi @jenilpatel264, this is a friendly reminder about your assignment to this issue.

[!WARNING] This issue will be automatically unassigned in 11 days if there's no activity.

Remember that you can ask the JabRef Guru or DeepWiki about anything regarding JabRef. Additionally, our contributing guide has hints on creating a pull request and a link to our Gitter chat.

How to keep your assignment

If you are working on it, you can prevent automatic unassignment by:

Submitting a draft pull request with your progress within 11 days
Asking for the 📌 Pinned label if you need more time

We appreciate your contribution and are here to help if needed!

Jun 14 '25 12:06 github-actions[bot]

We think that this issue was fixed. Please head to https://builds.jabref.org/main to download a development build and try it out.

For any feedback, add a comment to the pull request at https://github.com/JabRef/jabref/pull/13337.

Jun 17 '25 20:06 github-actions[bot]

Should we keep this issue open? Or a refined one is needed (ref. https://github.com/JabRef/jabref/pull/13337#pullrequestreview-2938191896)? @koppor

Jun 18 '25 08:06 subhramit

Reopened, the referring pr was just making the error message more clear but maybe did not fix the issue itself. Further testing and investigation required

Jun 18 '25 10:06 calixtus

jabref jabref copied to clipboard

IllegalArgumentException: URI is not absolute

JabRef version

Operating system

Details on version and operating system

Checked with the latest development build (copy version output from About dialog)

Steps to reproduce the behaviour

Appendix

📋 Assignment Update

⚠️ Issue Already Assigned

⚠️ Assignment Limit Reached

⏰ Assignment Reminder

jabref
jabref copied to clipboard